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- PDB-4wr7: Crystal structure of human carbonic anhydrase isozyme I with 2,3,... -

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Basic information

Entry
Database: PDB / ID: 4wr7
TitleCrystal structure of human carbonic anhydrase isozyme I with 2,3,5,6-Tetrafluoro-4-(propylthio)benzenesulfonamide.
ComponentsCarbonic anhydrase 1
KeywordsLYASE / drug design / benzenesulfonamide / metal-binding / lyase-lyase inhibitor complex
Function / homology
Function and homology information


hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen ...hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / extracellular exosome / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase ...Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-3TV / ACETATE ION / DI(HYDROXYETHYL)ETHER / Carbonic anhydrase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsManakova, E. / Smirnov, A. / Grazulis, S.
CitationJournal: Biophys.Chem. / Year: 2015
Title: Intrinsic thermodynamics of 4-substituted-2,3,5,6-tetrafluorobenzenesulfonamide binding to carbonic anhydrases by isothermal titration calorimetry.
Authors: Zubriene, A. / Smirnoviene, J. / Smirnov, A. / Morkunaite, V. / Michailoviene, V. / Jachno, J. / Juozapaitiene, V. / Norvaisas, P. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionOct 23, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 1
B: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,75611
Polymers57,6702
Non-polymers1,0869
Water9,296516
1
A: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3695
Polymers28,8351
Non-polymers5344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3876
Polymers28,8351
Non-polymers5525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.353, 72.034, 121.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Carbonic anhydrase 1 / Carbonate dehydratase I / Carbonic anhydrase B / CAB / Carbonic anhydrase I / CA-I


Mass: 28835.105 Da / Num. of mol.: 2 / Fragment: UNP residues 3-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00915, carbonic anhydrase

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Non-polymers , 6 types, 525 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Fragment: 2,3,5,6-Tetrafluoro-4-(propylthio)benzenesulfonamide
Mutation: ligandas / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-3TV / 2,3,5,6-tetrafluoro-4-(propylsulfanyl)benzenesulfonamide


Mass: 303.297 Da / Num. of mol.: 2 / Fragment: Zn / Source method: obtained synthetically / Formula: C9H9F4NO2S2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Fragment: ACETATE ION / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Fragment: DI(HYDROXYETHYL)ETHER / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Fragment: 1,2-ETHANEDIOL / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 0.1M TrisHCl (pH 8.5), 0.2M sodium acetate (pH 8.3), 28% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.826606 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826606 Å / Relative weight: 1
ReflectionResolution: 1.5→121.11 Å / Num. all: 85187 / Num. obs: 85187 / % possible obs: 96.8 % / Redundancy: 12.8 % / Biso Wilson estimate: 18.62 Å2 / Rpim(I) all: 0.019 / Rrim(I) all: 0.069 / Rsym value: 0.064 / Net I/av σ(I): 5.858 / Net I/σ(I): 17 / Num. measured all: 1093283
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueDiffraction-IDNet I/σ(I) obs% possible all
1.5-1.589.90.4120.37429859699790.130.410.37414.279.1
1.58-1.6813.30.3410.3182.3159286120160.090.340.3185.999.7
1.68-1.7913.30.2360.223.2150060112870.060.240.228.199.8
1.79-1.9413.40.1660.1554.2141100105360.050.170.15511.799.9
1.94-2.1213.20.1190.1115.712853197470.030.120.11116.699.9
2.12-2.3713.10.0920.086711558688300.030.090.08621.499.9
2.37-2.7413.30.0730.0678.510378678200.020.070.06725.999.8
2.74-3.3513.50.0580.05410.59030766970.020.060.05434.4100
3.35-4.7413.20.0470.04312.26907852380.010.050.04341.999.9
4.74-121.1112.20.0410.03710.43695330370.010.040.03737.799.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
AMoREphasing
SCALAdata scaling
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CAB

1cab
PDB Unreleased entry


Resolution: 1.5→61.91 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.199 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.842 / SU R Cruickshank DPI: 0.088 / SU Rfree: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.232 8555 10.1 %RANDOM
Rwork0.195 76532 --
obs0.199 85087 96.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.1 Å2 / Biso mean: 21.009 Å2 / Biso min: 9.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å20 Å2
2--2.05 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.5→61.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4038 0 61 516 4615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.024353
X-RAY DIFFRACTIONr_angle_refined_deg2.3681.9455937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1685547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87424.847196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24515691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3791514
X-RAY DIFFRACTIONr_chiral_restr0.190.2623
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213399
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 419 -
Rwork0.286 3572 -
all-3991 -
obs--62.07 %

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